## Usage

plotManh(A, alpha = 0.05, main, ...)

plotQQ(A, df = 1, main, ...)

## Arguments

- A
- An object of class
`solarAssoc`

.
- alpha
- A numeric value from 0 to 1, the p-value cut-off
for Bonferroni multiple-test correction.
The default value is 0.05.
- main
- A character string,
`main`

argument (title) to a plot function.
If the argument is missing, the title contains information about the model formula and the number of SNPs used for plotting.
- ...
- additional argument to a plot function.
- df
- An integer value, the degree of freedom.
The default value is 1.

## Description

Two Manhattan and quantile-quantile (QQ) plots
are standard to explore the results from association studies.

## Details

`plotManh`

function produces the Manhattan plot based on `qqman`

package.
The two red and blue lines, default in the original `manhattan`

function
of `qqman`

package, are preserved.
An additional black dashed line is added, that depicts the significance level
according to Bonferroni multiple-test correction with `alpha`

argument.

`plotQQ`

function produces the QQ plot based on the same `qqman`

package.

## Examples

## Not run:
# data(dat50)
#
# assoc <- solarAssoc(trait ~ 1, phenodata,
# snpdata = genodata, snpmap = snpdata, kinship = kin)
#
# plotManh(assoc) # equivalent to plot(assoc)
#
# plotQQ(assoc) # equivalent to plot(assoc, "qq")
#
# ## End(Not run)